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@Swennet said:
Anyway, I had a quick look for you and found the solution. In your forum folder open /applications/vanilla/js/discussion.js

Then on line 182 find
$(json.Data).appendTo('ul.Comments,.DiscussionTable').effect("highlight", {}, "slow");

Replace appendTo with prependTo. Done!

It should be noted however, that this is a 'hack'. You will have to edit this file manually every time you update Vanilla, because it will be overwritten on update.

Based on what you've found I have taken a look at the file and the context around that line is this:

if (gdn.definition('PrependNewComments') == '1') {
    $(json.Data).prependTo('ul.Comments,.DiscussionTable');
    $('ul.Comments li:first').effect("highlight", {}, "slow");
} else {
    $(json.Data).appendTo('ul.Comments,.DiscussionTable').effect("highlight", {}, "slow");

This seems like it should be possible to change the sort order by a definition. If you search for "PrependNewComments" you'll find that it is only used in the embed method of class.discussioncontroller.php:

// Ordering note for JS
if ($SortComments == 'desc') {
    $this->addDefinition('PrependNewComments', '1');
}

Since it is only used in embed(), we cannot influence this behavior simply by changing the config. We have to add that value "manually". Put the lines below in a plugin or a theme hooks file and you are done!

public function discussionController_render_before($sender, $args) {
    $sender->addDefinition('PrependNewComments', '1');
}